Hybrid somatic SV caller using long reads and short-read refinement for tumor–normal sequencing.

HapKled: a haplotype-aware structural variant calling approach for Oxford Nanopore sequencing data

Haplotype-Aware Structural Variant Detector

A collection of genomics software tools written in Rust

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

Detecting DNA methylation from PacBio CCS reads

A population-specific haplotype genome simulation tool developed based on pangenome data

A robust and high-resolution framework for detecting differentially methylated regions (DMRs) from second and third sequencing data.

SVHunter is a long-read-based structural variation detection through transformer model. SVHunter can detect and genotype DEL/INS/DUP/INV/TRA.

SVDF is a long-read-based structural variants caller uses deep learning network.

Pangenome-based structural variation caller

A comprehensive DNA methylation atlas for the Chinese population through nanopore long-read sequencing of 106 individuals

cuteSV-OL: a real-time structural variation detection framework for nanopore sequencing devices

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads

Lightweight mosaic/somatic SV caller for long reads (WIP)

This repo is for backup only. Please check the parent repo for details.

Haplotype-specific somatic copy number aberrations/profiling from long reads sequencing data

Tumor-normal variant calling workflow using HiFi reads

Regenotyping structural variants through an accurate and efficient force-calling method

vcfdist: Accurately benchmarking phased variant calls

A program to call variants from genome alignment

Somatic structural variant caller for long-read data

A tool for somatic structural variant calling using long reads

Copy number caller for long read data including SNV utilization

Wally: Visualization of aligned sequencing reads and contigs

MethPhaser: methylation-based haplotype phasing of human genomes